hjxdl 0.1.13__py3-none-any.whl → 0.1.15__py3-none-any.whl

hdl/datasets/defined_BaseFeatures.fdef

@@ -0,0 +1,236 @@
+# $Id$
+#
+# RDKit base fdef file.
+# Created by Greg Landrum
+#
+
+AtomType NDonor [#7&!H0]
+AtomType AmideN [$(N-C(=O))]
+AtomType SulfonamideN [$([N;H0]S(=O)(=O))]
+# AtomType NDonor [$([Nv3](-C)(-C)-C)]
+
+# consider tautomer
+# AtomType NDonor [$(n[n;H1]),$(nc[n;H1])]
+
+AtomType ChalcDonor [O,S;H1;+0]
+DefineFeature SingleAtomDonor [{NDonor},{ChalcDonor}]
+  Family Donor
+  Weights 1
+EndFeature
+
+# aromatic N, but not indole or pyrole or fusing two rings
+AtomType NAcceptor [n;X2;H0]
+# AtomType NAcceptor [$([N;H0]#[C&v4])]
+# tertiary nitrogen adjacent to aromatic carbon
+
+# AtomType NAcceptor [N&v3;H0;$(Nc)]
+AtomType NAcceptor [$(N=,#*);X2,X1]
+
+# removes thioether and nitro oxygen
+AtomType ChalcAcceptor [O;!$(O=N-*);!$(*-N=O)] 
+# Atomtype ChalcAcceptor [O;-;!$(*-N=O)] 
+
+# Removed aromatic sulfur from ChalcAcceptor definition
+Atomtype ChalcAcceptor [o;+0]
+
+# Hydroxyls and acids
+AtomType Hydroxyl [O;H1;v2]
+
+# F is an acceptor so long as the C has no other halogen neighbors. This is maybe
+# a bit too general, but the idea is to eliminate things like CF3
+AtomType HalogenAcceptor [F;$(F-[#6]);!$(FC[F,Cl,Br,I])]
+
+DefineFeature SingleAtomAcceptor [{Hydroxyl},{ChalcAcceptor},{NAcceptor},{HalogenAcceptor}]
+  Family Acceptor
+  Weights 1
+EndFeature
+
+# this one is delightfully easy:
+#DefineFeature AcidicGroup [C,S](=[O,S,P])-[O;H1,H0&-1]
+#  Family NegIonizable
+#  Weights 1.0,1.0,1.0
+#EndFeature
+
+DefineFeature AcidicGroup [O;H0&-1,$(O=[C,P,S][O-])]
+   Family NegIonizable
+   Weights 1.0
+EndFeature
+
+AtomType Carbon_NotDouble [C;!$(C=*)]
+AtomType BasicNH2 [$([N;H2&+0][{Carbon_NotDouble}])]
+AtomType BasicNH1 [$([N;H1&+0]([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
+AtomType PosNH3 [$([N;H3&+1][{Carbon_NotDouble}])]
+AtomType PosNH2 [$([N;H2&+1]([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
+AtomType PosNH1 [$([N;H1&+1]([{Carbon_NotDouble}])([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
+AtomType BasicNH0 [$([N;H0&+0]([{Carbon_NotDouble}])([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
+AtomType QuatN [$([N;H0&+1]([{Carbon_NotDouble}])([{Carbon_NotDouble}])([{Carbon_NotDouble}])[{Carbon_NotDouble}])]
+
+DefineFeature BasicGroup [$([#7;H3,H2,H1;+1]),$([#7]=[#6][#7;H3,H2,H1;+1])]
+   Family PosIonizable
+   Weights 1.0
+EndFeature
+
+#DefineFeature BasicGroup [{BasicNH2},{BasicNH1},{BasicNH0};!$(N[a])]
+#  Family PosIonizable
+#  Weights 1.0
+#EndFeature
+
+# 14.11.2007 (GL): add !$([N+]-[O-]) constraint so we don't match
+# nitro (or similar) groups
+#DefineFeature PosN [#7;+;!$([N+]-[O-])]
+# Family PosIonizable
+# Weights 1.0
+#EndFeature
+
+# imidazole group can be positively charged (too promiscuous?)
+#DefineFeature Imidazole c1ncnc1
+#  Family PosIonizable
+#  Weights 1.0,1.0,1.0,1.0,1.0
+#EndFeature
+# guanidine group is positively charged (too promiscuous?)
+#DefineFeature Guanidine NC(=N)N
+#  Family PosIonizable
+#  Weights 1.0,1.0,1.0,1.0
+#EndFeature
+
+# the LigZn binder features were adapted from combichem.fdl
+DefineFeature ZnBinder1 [S;D1]-[#6]
+  Family ZnBinder
+  Weights 1,0
+EndFeature
+DefineFeature ZnBinder2 [#6]-C(=O)-C-[S;D1]
+  Family ZnBinder
+  Weights 0,0,1,0,1
+EndFeature
+DefineFeature ZnBinder3 [#6]-C(=O)-C-C-[S;D1]
+  Family ZnBinder
+  Weights 0,0,1,0,0,1
+EndFeature
+
+DefineFeature ZnBinder4 [#6]-C(=O)-N-[O;D1]
+  Family ZnBinder
+  Weights 0,0,1,0,1
+EndFeature
+DefineFeature ZnBinder5 [#6]-C(=O)-[O;D1]
+  Family ZnBinder
+  Weights 0,0,1,1
+EndFeature
+DefineFeature ZnBinder6 [#6]-P(=O)(-O)-[C,O,N]-[C,H]
+  Family ZnBinder
+  Weights 0,0,1,1,0,0
+EndFeature
+
+
+# aromatic rings of various sizes:
+#
+# Note that with the aromatics, it's important to include the ring-size queries along with
+# the aromaticity query for two reasons:
+#   1) Much of the current feature-location code assumes that the feature point is 
+#      equidistant from the atoms defining it. Larger definitions like: a1aaaaaaaa1 will actually 
+#      match things like 'o1c2cccc2ccc1', which have an aromatic unit spread across multiple simple
+#      rings and so don't fit that requirement.
+#   2) It's *way* faster.
+#
+
+#
+# 21.1.2008 (GL): update ring membership tests to reflect corrected meaning of
+# "r" in SMARTS parser
+#
+AtomType AromR4 [a;r4,!R1&r3]
+DefineFeature Arom4 [{AromR4}]1:[{AromR4}]:[{AromR4}]:[{AromR4}]:1
+ Family Aromatic
+ Weights 1.0,1.0,1.0,1.0
+EndFeature
+AtomType AromR5 [a;r5,!R1&r4,!R1&r3]
+DefineFeature Arom5 [{AromR5}]1:[{AromR5}]:[{AromR5}]:[{AromR5}]:[{AromR5}]:1
+ Family Aromatic
+ Weights 1.0,1.0,1.0,1.0,1.0
+EndFeature
+AtomType AromR6 [a;r6,!R1&r5,!R1&r4,!R1&r3]
+DefineFeature Arom6 [{AromR6}]1:[{AromR6}]:[{AromR6}]:[{AromR6}]:[{AromR6}]:[{AromR6}]:1
+ Family Aromatic
+ Weights 1.0,1.0,1.0,1.0,1.0,1.0
+EndFeature
+AtomType AromR7 [a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]
+DefineFeature Arom7 [{AromR7}]1:[{AromR7}]:[{AromR7}]:[{AromR7}]:[{AromR7}]:[{AromR7}]:[{AromR7}]:1
+ Family Aromatic
+ Weights 1.0,1.0,1.0,1.0,1.0,1.0,1.0
+EndFeature
+AtomType AromR8 [a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]
+DefineFeature Arom8 [{AromR8}]1:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:1
+ Family Aromatic
+ Weights 1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0
+EndFeature
+
+# hydrophobic features
+# any carbon that is not bonded to a polar atom is considered a hydrophobe
+# 
+# 23.11.2007 (GL): match any bond (not just single bonds); add #6 at
+#  beginning to make it more efficient
+AtomType Carbon_Polar [#6;$([#6]~[#7,#8,#9])]
+# 23.11.2007 (GL): don't match charged carbon
+AtomType Carbon_NonPolar [#6;+0;!{Carbon_Polar}]
+
+DefineFeature ThreeWayAttach [D3,D4;{Carbon_NonPolar}]
+  Family Hydrophobe
+  Weights 1.0
+EndFeature
+
+DefineFeature ChainTwoWayAttach [R0;D2;{Carbon_NonPolar}]
+  Family Hydrophobe
+  Weights 1.0
+EndFeature
+
+DefineFeature AnyAtom [*]
+  Family Any
+  Weights 1.0
+EndFeature
+
+# hydrophobic atom
+AtomType Hphobe [c,s,S&H0&v2,Br,I,{Carbon_NonPolar}]
+AtomType RingHphobe [R;{Hphobe}]
+
+# nitro groups in the RD code are always: *-[N+](=O)[O-]
+DefineFeature Nitro2 [N;D3;+](=O)[O-]
+  Family LumpedHydrophobe
+  Weights 1.0,1.0,1.0
+EndFeature
+
+#
+# 21.1.2008 (GL): update ring membership tests to reflect corrected meaning of
+# "r" in SMARTS parser
+#
+AtomType Ring6 [r6,!R1&r5,!R1&r4,!R1&r3]
+DefineFeature RH6_6 [{Ring6};{RingHphobe}]1[{Ring6};{RingHphobe}][{Ring6};{RingHphobe}][{Ring6};{RingHphobe}][{Ring6};{RingHphobe}][{Ring6};{RingHphobe}]1
+  Family LumpedHydrophobe
+  Weights 1.0,1.0,1.0,1.0,1.0,1.0
+EndFeature
+
+AtomType Ring5 [r5,!R1&r4,!R1&r3]
+DefineFeature RH5_5 [{Ring5};{RingHphobe}]1[{Ring5};{RingHphobe}][{Ring5};{RingHphobe}][{Ring5};{RingHphobe}][{Ring5};{RingHphobe}]1
+  Family LumpedHydrophobe
+  Weights 1.0,1.0,1.0,1.0,1.0
+EndFeature
+
+AtomType Ring4 [r4,!R1&r3]
+DefineFeature RH4_4 [{Ring4};{RingHphobe}]1[{Ring4};{RingHphobe}][{Ring4};{RingHphobe}][{Ring4};{RingHphobe}]1
+  Family LumpedHydrophobe
+  Weights 1.0,1.0,1.0,1.0
+EndFeature
+
+AtomType Ring3 [r3]
+DefineFeature RH3_3 [{Ring3};{RingHphobe}]1[{Ring3};{RingHphobe}][{Ring3};{RingHphobe}]1
+  Family LumpedHydrophobe
+  Weights 1.0,1.0,1.0
+EndFeature
+
+DefineFeature tButyl [C;!R](-[CH3])(-[CH3])-[CH3]
+  Family LumpedHydrophobe
+  Weights 1.0,0.0,0.0,0.0
+EndFeature
+
+DefineFeature iPropyl [CH;!R](-[CH3])-[CH3]
+  Family LumpedHydrophobe
+  Weights 1.0,1.0,1.0
+EndFeature
+

hdl/datasets/route_template.json

@@ -0,0 +1,113 @@
+
+[
+    {
+        "mol_id": {
+            "id_type": "CAS",
+            "id_value": "111-222-333",
+            "smiles": "",
+            "routes": [
+                {   
+                    "rxn_template": "",
+                    "rxn_type": "",
+                    "yield": 0.0,
+                    "children": [
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        },
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        }
+                    ]
+                },
+                {   
+                    "rxn_template": "",
+                    "rxn_type": "",
+                    "yield": 0.0,
+                    "children": [
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        },
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        }
+                    ]
+                }
+            ]
+        }
+    },
+    {
+        "mol_id": {
+            "id_type": "CAS",
+            "id_value": "111-222-333",
+            "smiles": "",
+            "routes": [
+                {   
+                    "rxn_template": "",
+                    "rxn_type": "",
+                    "yield": 0.0,
+                    "children": [
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        },
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        }
+                    ]
+                },
+                {   
+                    "rxn_template": "",
+                    "rxn_type": "",
+                    "yield": 0.0,
+                    "children": [
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        },
+                        {
+                            "mol_id": {
+                                "id_type": "CAS",
+                                "id_value": "111-222-333",
+                                "smiles": "",
+                                "routes": []
+                            }
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+]